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E39 (1997 - 2003) The BMW 5-Series (E39 chassis) was introduced in the United States as a 1997 model year car and lasted until the 2004 when the E60 chassis was released. The United States saw several variations including the 525i, 528i, 530i and 540i. -- View the E39 Wiki

it goes away when revved to 4000 so anything loose would keep making the noise I think.
I don't have any experience with VANOS so that is what I thought it might be.
In any case I work in Africa so the fix will have to wait!

Many V8s were troubled with rod bearing wear. BMW did replace the bearings upon complaint. BMW said that the noise was not a problem, and would not compromise engine longevity - difficult for me to believe.

The noise would be a deeper knock, inside the engine, rather than marbles in a tin can.

Check your spark plugs to make sure they are all snug. I had a loud knock/tick that drove me nuts. I found 2 spark plugs that were loose, tightened them up and it's nice and quiet since. This has been known to happen on these engines and many posts about this can be found (when I searched I was very suprised how many people fixed the ticking/knocking by finding a loose plug or two and then tightening them). Folks seem to say the OEM Bosch plugs are notorious for "backing out" and they recommend another brand (can't remember). I have fairly new Bosch plugs but I just check them every once in a while ever since I had this issue.
Good luck!

SUBJECT:
Water Pump Impeller Shaft Binding
MODEL:
E31 with M62 engine up to 8/97,
E38 and E39 with M62 engines up to 8/98
Situation:
A customer complaint of an intermittent rough idle may be received with the following operating conditions:
- Engine at operating temperature
- Air conditioning switched on
- Transmission in drive
Cause:
The intermittent rough engine idle under the above conditions may be caused by a binding water pump impeller shaft.
Due to the excessive engine load at idle and / or an internal water pump noise (chatter) detected by the knock sensors the DME causes the ignition timing to retard in some cases dipping as much as -18°KW (crankshaft angle) at idle to compensate for this problem thus resulting in a rough idle condition.

The injection and air mass signals are also higher than normal at idle when the rough idle occurs.

The table below indicates the nominal values for a normal running engine versus the values on a rough running engine with a binding water pump impeller shaft at idle:

Description Normal Running Engine Rough Running Engine
Ignition Timing 8 to 15°KW 0 to -18°KW
Injection Signal 3 to 4.5 ms 5 to 7 ms
Mass Air Flow Sensor 20 to 30 kg/h 35 to 55 kg/h
Signal
Correction:
If a customer complaint of an intermittent rough idle is received as described above and the water pump impeller shaft is found to be binding, the water pump should be replaced as outlined in the repair manual group 11, section 11 51.
Procedure:
When troubleshooting for a binding water pump impeller shaft:
- Remove the water pump / generator drive belt (see repair manual group 11, section 11 28).
- Rotate the water pump pulley by hand.
Note: The impeller shaft should rotate without applying excessive force. A slight resistance will be felt and is acceptable (as felt on a new water pump).
- To qualify a binding impeller shaft - remove the water pump pulley and check the impeller shaft bearing assembly located in the pump housing behind the pulley flange.
The impeller shaft bearing when properly seated is recessed in the pump housing approximately 1-2 mm. The impeller shaft bearing on a binding water pump protrudes out of the water pump housing approximately 2-3 mm.

This is just a thought from a newbie here. I had the same issue. I replaced the water pump and tstat thinking it may have been the problem. After starting the car back up, same noise. But after successfully bleeeding the air out of the system, the noise went away. Did you happen to replace any cooling system related sensors on the hoses ? I am just wondering if any air in the cooling system could be a possible issue. If im wrong, oh well, I am sure I will hear about it But if it turns out to be a legitimate diagnosis, I am a happy camper. Of course there may already be a theory on this but I am too lazy to search for it right now. Back is killing me from the wp replacement last night!!!

Many V8s were troubled with rod bearing wear. BMW did replace the bearings upon complaint. BMW said that the noise was not a problem, and would not compromise engine longevity - difficult for me to believe.

The noise would be a deeper knock, inside the engine, rather than marbles in a tin can.

Try running a heavier oil, like 20W50 ( or Mobil 1 0W40).

After a spirited day of driving, my engine has developed a knocking sound. Like the OP, it goes away when I accelerate. It sounds deep inside the engine. What can it be? Can bad gas make it knock?

__________________

"The more you know, the more you don't know," Dave Chappelle
"Man is an emotional animal, occasionally rational; and through his feelings he can be deceived to his heart's content"-Durant

Check your spark plugs to make sure they are all snug. I had a loud knock/tick that drove me nuts. I found 2 spark plugs that were loose, tightened them up and it's nice and quiet since. This has been known to happen on these engines and many posts about this can be found (when I searched I was very suprised how many people fixed the ticking/knocking by finding a loose plug or two and then tightening them). Folks seem to say the OEM Bosch plugs are notorious for "backing out" and they recommend another brand (can't remember). I have fairly new Bosch plugs but I just check them every once in a while ever since I had this issue.
Good luck!

This is a long shot but adding to this thought: a friend of mine has a 97 Outback which developed a loud knocking sound last spring, the cause of which we could not identify. After he began removing parts from the engine, he discovered a cracked insulator on a spark plug. They were installed new ~9K miles prior. He installed four new plugs and the car has been running perfectly.

I think it's fairly normal for our M62's to have some knocking noise..... mine has a little, not like yours but I've heard some that are much louder than yours. These engines are known to be noisy so I wouldn't worry too much about it. Make sure your spark plugs are all tight and oil level is correct..... other than that you will drive yourself crazy trying to fix it. Possibly replace the timing chain tensioner and try thicker oil come spring/summer.

I am familiar with rod knocks. Anyone else ever have a Triumph Stag? A distinguishing feature of worn rod bearings is a knock that is almost inaudible when accelerating but much louder when you get off the gas and the motor is slowing down. There's no load on the rod bearings then and they're free to rattle around. May or may not be too noisy at idle. This pattern could apply to other problems too, but if it's not doing this it probably isn't a rod knock.

Well I found out what it was making the noise.
Just about all the plastic on the chain guides was gone. chain was rubbing on cover.
I have it all apart now and just got the parts so with any luck I will be back on the toad soon.

Everything back together. Connected charger to posts and voila! doors opened! it was like magic!
Started to fill overflow reservoir with coolant and it was leaking out bottom some where. Have to go back underneath to see what the hell that is all about!
hope the oil system works better than that!